I think DMC3, and the DMC1 game and novel would comprise the "Kamiya Canon," because were the only things that had input from him on the story and characters. Everything else is sort of a crapshoot.
I think the DMC3 manga was denied canon, because it contradicted certain things from DMC3 (like when Dante and Lady see each other and such), and the DMC4 novel is supposed to be taken as canon because...I dunno, it was written by the guy who wrote DMC4's scenario, it was cleared by Capcom, and it was the novelization of DMC4. But they still never outright stated Vergil was Nero's father, and really only strengthened a lot of hints about Nero being a descendant of Sparda.
I think the DMC3 manga was denied canon, because it contradicted certain things from DMC3 (like when Dante and Lady see each other and such), and the DMC4 novel is supposed to be taken as canon because...I dunno, it was written by the guy who wrote DMC4's scenario, it was cleared by Capcom, and it was the novelization of DMC4. But they still never outright stated Vergil was Nero's father, and really only strengthened a lot of hints about Nero being a descendant of Sparda.